Timing of Blood Sample Processing Affects the Transcriptomic and Epigenomic Profiles in CD4+ T-cells of Atopic Subjects
Optimal pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4+...
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| Published in | Cells (Basel, Switzerland) Vol. 11; no. 19; p. 2958 |
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| Main Authors | , , , , , , , , , , , , |
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22.09.2022
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| Abstract | Optimal pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4+ T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, CD4+ T-cells were isolated from the first blood sample within 2 h (immediate) or from the second blood sample after 24 h storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed CD4+ T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed CD4+ T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood CD4+ T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operation procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended. |
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| AbstractList | Optimal pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4+ T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, CD4+ T-cells were isolated from the first blood sample within 2 h (immediate) or from the second blood sample after 24 h storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed CD4+ T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed CD4+ T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood CD4+ T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operation procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended. Optimal pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4+ T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, CD4+ T-cells were isolated from the first blood sample within 2 h (immediate) or from the second blood sample after 24 h storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed CD4+ T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed CD4+ T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood CD4+ T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operation procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended.Optimal pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4+ T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, CD4+ T-cells were isolated from the first blood sample within 2 h (immediate) or from the second blood sample after 24 h storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed CD4+ T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed CD4+ T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood CD4+ T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operation procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended. Optimal pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4 + T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, CD4 + T-cells were isolated from the first blood sample within 2 h (immediate) or from the second blood sample after 24 h storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed CD4 + T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed CD4 + T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood CD4 + T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operation procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended. Optimal pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4[sup.+] T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, CD4[sup.+] T-cells were isolated from the first blood sample within 2 h (immediate) or from the second blood sample after 24 h storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed CD4[sup.+] T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed CD4[sup.+] T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood CD4[sup.+] T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operation procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended. |
| Audience | Academic |
| Author | Conca, Raffaele Laubhahn, Kristina Schaub, Bianca Hansen, Gesine Jirmo, Adan C. Alhamdan, Fahd Happle, Christine Potaczek, Daniel P. Habener, Anika Chung, Ho-Ryun Grychtol, Ruth Garn, Holger Thölken, Clemens |
| AuthorAffiliation | 2 Department of Medicine, Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA 6 Bioscientia MVZ Labor Mittelhessen GmbH, D-35394 Gießen, Germany 1 Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Medical Faculty, Philipps University of Marburg, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, D-35043 Marburg, Germany 4 Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL) and the Cluster of Excellence RESIST (EXC 2155), D-30625 Hannover, Germany 5 Institute of Medical Bioinformatics and Biostatistics, Medical Faculty, Philipps University of Marburg, D-35032 Marburg, Germany 3 Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children’s Hospital, Univers |
| AuthorAffiliation_xml | – name: 2 Department of Medicine, Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA – name: 1 Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Medical Faculty, Philipps University of Marburg, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, D-35043 Marburg, Germany – name: 5 Institute of Medical Bioinformatics and Biostatistics, Medical Faculty, Philipps University of Marburg, D-35032 Marburg, Germany – name: 3 Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig Maximilian University (LMU) of Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), D-80337 Munich, Germany – name: 6 Bioscientia MVZ Labor Mittelhessen GmbH, D-35394 Gießen, Germany – name: 4 Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL) and the Cluster of Excellence RESIST (EXC 2155), D-30625 Hannover, Germany |
| Author_xml | – sequence: 1 givenname: Fahd surname: Alhamdan fullname: Alhamdan, Fahd – sequence: 2 givenname: Kristina surname: Laubhahn fullname: Laubhahn, Kristina – sequence: 3 givenname: Christine surname: Happle fullname: Happle, Christine – sequence: 4 givenname: Anika surname: Habener fullname: Habener, Anika – sequence: 5 givenname: Adan C. orcidid: 0000-0002-4693-0081 surname: Jirmo fullname: Jirmo, Adan C. – sequence: 6 givenname: Clemens orcidid: 0000-0003-4328-9193 surname: Thölken fullname: Thölken, Clemens – sequence: 7 givenname: Raffaele surname: Conca fullname: Conca, Raffaele – sequence: 8 givenname: Ho-Ryun surname: Chung fullname: Chung, Ho-Ryun – sequence: 9 givenname: Gesine surname: Hansen fullname: Hansen, Gesine – sequence: 10 givenname: Daniel P. orcidid: 0000-0003-0324-8506 surname: Potaczek fullname: Potaczek, Daniel P. – sequence: 11 givenname: Bianca orcidid: 0000-0003-1652-8873 surname: Schaub fullname: Schaub, Bianca – sequence: 12 givenname: Ruth surname: Grychtol fullname: Grychtol, Ruth – sequence: 13 givenname: Holger orcidid: 0000-0002-5178-4023 surname: Garn fullname: Garn, Holger |
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| SubjectTerms | Acetylation Atopy Biobanks Blood CD4 antigen CD4+ T-cells ChIP sequencing Chromatin Cohort analysis Epigenetic inheritance Epigenetics Gene expression Genetic aspects Genomes Hay fever Health aspects histone modifications Histones Immunoprecipitation Lymphocytes T Medical examination Medical research Medicine, Experimental Pediatrics Peripheral blood Rhinitis RNA T cells Transcriptomics |
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| Title | Timing of Blood Sample Processing Affects the Transcriptomic and Epigenomic Profiles in CD4+ T-cells of Atopic Subjects |
| URI | https://www.proquest.com/docview/2724215545 https://www.proquest.com/docview/2725193872 https://pubmed.ncbi.nlm.nih.gov/PMC9563434 https://doaj.org/article/6bb792f3ee8248c78b423e4beba9dd68 |
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